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A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer

In: High Performance Computing in Science and Engineering ' 18

Author

Listed:
  • Goutam Mukherjee

    (Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group
    Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University)

  • Prajwal Nandekar

    (Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group
    Center for Molecular Biology (ZMBH), Heidelberg University)

  • Ghulam Mustafa

    (Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group)

  • Stefan Richter

    (Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group)

  • Rebecca C. Wade

    (Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group
    Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University
    Center for Molecular Biology (ZMBH), Heidelberg University)

Abstract

We describe a transferable multiresolution computational approach to build and simulate complexes of two proteins—cytochrome P450 (CYP) and CYP reductase (CPR)—in a membrane bilayer using Brownian dynamics (BD) and all-atom molecular dynamics (MD) simulations. Our benchmarks showed that MD simulations of these systems could be carried out efficiently with up to 180 nodes (4320 cores) using NAMD version 2.12. Our results provide a basis for defining the ensemble of electron transfer-competent arrangements of CYP-CPR-membrane complexes and for understanding differences in the interactions with CPR of different CYPs, which have implications for CYP-mediated drug metabolism and the exploitation of CYPs as drug targets. This work was carried out in the DYNATHOR (DYNAmics of THe complex of cytOchrome P450 and cytochrome P450 Reductase in a phospholipid bilayer) project at HLRS.

Suggested Citation

  • Goutam Mukherjee & Prajwal Nandekar & Ghulam Mustafa & Stefan Richter & Rebecca C. Wade, 2019. "A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer," Springer Books, in: Wolfgang E. Nagel & Dietmar H. Kröner & Michael M. Resch (ed.), High Performance Computing in Science and Engineering ' 18, pages 505-514, Springer.
    • Handle: RePEc:spr:sprchp:978-3-030-13325-2_32
    DOI: 10.1007/978-3-030-13325-2_32
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